Fixing non-manifold edge for 3d printing
While removing  doubles with a high merge distance of 0.1 or more will remove some of the problem, fixing the non-manifold issue manually will take a very long time as you need to fix each and every errant vertex.

However, if you don't need to maintain the exact same mesh and can live with a very very close reconstruction of it, you can fix the non-manifold issue automatically by using the remesh modifier, and then the decimate modifier to reduce the polycount back to sanity.

Here's the setup:


After adding the modifiers with the parameter values specified above, you can either directly export to STL (File --> Export --> Stl) or apply the modifiers and then export.